Due to a problem in the Quartus® Prime software version 16.1 and earlier, when boot option Nios® II processor application executes in place from EPCQ flash is selected, you may see the Start Address of Nios II software Hex Data set to 0x00000000 when the HEX Data Properties is set to Absolute addressing mode in Convert Programming File utility.
This problem does not occur when boot option Nios II processor application is copied from EPCQ flash to RAM using boot copier is selected.
To work around this problem, select Relative addressing mode in HEX Data Properties and set the start address to the Nios II Processor Reset vector offset as configured in Qsys.
This problem is scheduled to be fixed in a future version of the Quartus Prime software.